This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The study of protein phosphorylation by mass spectrometry often requires enrichment of low abundance proteins and peptides from complex biological samples. One method of enrichment is immobilized metal-ion affinity chromatography (IMAC). Non-specific binding is a complication in IMAC enrichment, and can be reduced by treatment with methanolic HCl to esterify peptide acidic groups. The side reactions that occur during esterification have been investigated to document the conditions that lead to their occurrence and minimize their impact. The use of alternative metal oxides has been explored, as well as precipitation of phosphopeptides/proteins with calcium salts. Each procedure has been optimized by use of standards and then applied to the analysis of samples from biological sources. Procedures have been developed for efficient detection of phosphopeptides during LC/MS analysis on the LTQ-Orbitrap tandem MS. A new dissociation method, electron transfer dissociation (ETD) is being evaluated for use on the Bruker ion trap and has provided excellent, site-specific results for standards and previously characterized peptides. This system will now be used for the analysis of phosphopeptides for which the sites are as yet unknown.